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Bumped all the container versions #257

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8 changes: 4 additions & 4 deletions modules/msk/generatemutfasta/main.nf
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
process GENERATEMUTFASTA {
tag "$meta.id"
label 'process_single'
container "ghcr.io/mskcc-omics-workflows/neoantigen-utils-base:1.4.0"
container "ghcr.io/mskcc-omics-workflows/neoantigen-utils-base:1.6.0"

input:
tuple val(meta), path(inputMaf)
Expand Down Expand Up @@ -32,13 +32,13 @@ process GENERATEMUTFASTA {

mkdir ${prefix}_out

MUTALYZER_SETTINGS="\$(pwd)/config.txt" generateMutFasta.py --sample_id ${prefix} \
MUTALYZER_SETTINGS="\$(pwd)/config.txt" generate_mut_fasta.py --sample_id ${prefix} \
--output_dir ${prefix}_out \
--maf_file ${inputMaf}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
generateMutFasta: \$(echo \$(generateMutFasta.py -v))
generateMutFasta: \$(echo \$(generate_mut_fasta.py -v))
mutalyzer: \$(echo \$(mutalyzer_normalizer -v | tr '\n' ' ' | awk '{print \$3}'))
END_VERSIONS
"""
Expand All @@ -54,7 +54,7 @@ process GENERATEMUTFASTA {
touch ${prefix}_out/${prefix}_generate_mut_fasta.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":
generateMutFasta: \$(echo \$(generateMutFasta.py -v))
generateMutFasta: \$(echo \$(generate_mut_fasta.py -v))
mutalyzer: \$(echo \$(mutalyzer_normalizer -v | tr '\n' ' ' | awk '{print \$3}'))
END_VERSIONS
"""
Expand Down
2 changes: 1 addition & 1 deletion modules/msk/mutalyzer/normalizer/main.nf
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
process MUTALYZER_NORMALIZER {
tag "$meta.id"
label 'process_single'
container "ghcr.io/mskcc-omics-workflows/neoantigen-utils-base:1.4.0"
container "ghcr.io/mskcc-omics-workflows/neoantigen-utils-base:1.6.0"

input:
tuple val(meta), val(hgvs_description)
Expand Down
2 changes: 1 addition & 1 deletion modules/msk/mutalyzer/retriever/main.nf
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
process MUTALYZER_RETRIEVER {
tag "$meta.id"
label 'process_medium'
container "ghcr.io/mskcc-omics-workflows/neoantigen-utils-base:1.4.0"
container "ghcr.io/mskcc-omics-workflows/neoantigen-utils-base:1.6.0"

input:
tuple val(meta), path(fasta), path(gff3)
Expand Down
293 changes: 0 additions & 293 deletions modules/msk/neoantigenediting/aligntoiedb/resources/usr/bin/align_neoantigens_to_IEDB.py
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4 changes: 2 additions & 2 deletions modules/msk/neoantigenediting/computefitness/main.nf
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Expand Up @@ -3,8 +3,8 @@ process NEOANTIGENEDITING_COMPUTEFITNESS {
label 'process_medium'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker://ghcr.io/mskcc-omics-workflows/neoantigen-editing:1.3':
'ghcr.io/mskcc-omics-workflows/neoantigen-editing:1.3' }"
'docker://ghcr.io/mskcc-omics-workflows/neoantigen-editing:1.1':
'ghcr.io/mskcc-omics-workflows/neoantigen-editing:1.1' }"

input:
tuple val(meta), path(patient_data), path(alignment_file)
Expand Down
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